Your abstract for the HUPO2012 conference was submitted on 5/3/2012.The log number for your abstract is 294. | ||||||||||||||||||||
| Analysis of Protein Networks | ||||||||||||||||||||
| Mark Gerstein | ||||||||||||||||||||
| Yale Comp. Bio., New Haven, CT | ||||||||||||||||||||
| Abstract My talk will be concerned with understanding protein function on a genomic scale. My lab approaches this through the prediction and analysis of biological networks, focusing on protein-protein interaction and transcription-factor-target ones. I will describe how these networks can be determined through integration of many genomic features and how they can be analyzed in terms of various topological statistics. In particular, I will discuss a number of recent analyses: (1) Improving the prediction of molecular networks through systematic training-set expansion; (2) Showing how the analysis of biochemical pathways across environments potentially allows them to act as biosensors; (3) Analyzing the structure of the regulatory network indicates that it has a hierarchical layout with the "middle-managers" acting as information bottlenecks; (4) Integrating the protein-interaction network with molecular structures and motions; (5) Showing the some motions are conflicting with protein-protein interactions and (6) Creating practical web-based tools for the analysis of these networks (DynaSIN and tYNA).
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Thursday, October 4, 2012
2012 HUPO Abstract Entry Confirmation 294
Saturday, May 19, 2012
Re: Abstract for talk at CBCB Symposium at U Del ((* i0udcbcbrs *))
Many thanks Mark, We are looking forward to your inspiring talk :-)
Best, Cathy
On 5/19/2012 12:04 AM, Mark Gerstein wrote:
> TITLE:
>
> Molecular Networks: The Next-generation Annotation for Personal Genomes
>
> Mark Gerstein
>
> Yale University
>
> My talk will be concerned the analysis of networks and the use of
> networks as a "next-generation annotation" for interpreting personal
> genomes. I will initially describe current approaches to genome
> annotation in terms of one-dimension browser tracks. Then I will
> describe various aspects of networks. In particular, I will touch on
> the following topics: (1) I will show how analyzing the structure of
> the regulatory network indicates that it has a hierarchical layout
> with the "middle-managers" acting as information-flow bottlenecks and
> with more "influential" TFs on top. (2) I will show that most human
> variation occurs at the periphery of the network. (3) I will compare
> the topology and variation of the regulatory network to the call graph
> of a computer operating system, showing that they have different
> patterns of variation. (4) I will talk about web-based tools for the
> analysis of networks (TopNet and tYNA).
>
> http://networks.gersteinlab.org
> http://tyna.gersteinlab.org
>
> Comparing genomes to computer operating systems in terms of the
> topology and evolution of their regulatory control networks.
> KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
> Acad Sci U S A 107:9186-91.
>
> Analysis of diverse regulatory networks in a hierarchical context
> shows consistent tendencies for collaboration in the middle levels.
> N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
>
> Positive selection at the protein network periphery: evaluation in
> terms of structural constraints and cellular context.
> PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
>
> The tYNA platform for comparative interactomics: a web tool for
> managing, comparing and mining multiple networks.
> KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
--
Cathy H. Wu, Ph.D.
Edward G. Jefferson Chair of Bioinformatics& Computational Biology
Department of Computer& Information Sciences
Department of Biological Sciences
Director, Center for Bioinformatics& Computational Biology (CBCB)
Director, Master's Programs in Bioinformatics& Computational Biology
Director, Protein Information Resource (PIR)
Delaware Biotechnology Institute
University of Delaware
15 Innovation Way, Suite 205
Newark, DE 19711-5449
Email: wuc@udel.edu
Phone: 302-831-8869; Fax: 302-831-4841
Adm Assistant: Susan Phipps
Email: phipps@dbi.udel.edu
Phone: 302-831-0161
CBCB home: http://bioinformatics.udel.edu
Master's programs: http://bioinformatics.udel.edu/Education
PIR Home: http://ProteinInformationResource.org
Best, Cathy
On 5/19/2012 12:04 AM, Mark Gerstein wrote:
> TITLE:
>
> Molecular Networks: The Next-generation Annotation for Personal Genomes
>
> Mark Gerstein
>
> Yale University
>
> My talk will be concerned the analysis of networks and the use of
> networks as a "next-generation annotation" for interpreting personal
> genomes. I will initially describe current approaches to genome
> annotation in terms of one-dimension browser tracks. Then I will
> describe various aspects of networks. In particular, I will touch on
> the following topics: (1) I will show how analyzing the structure of
> the regulatory network indicates that it has a hierarchical layout
> with the "middle-managers" acting as information-flow bottlenecks and
> with more "influential" TFs on top. (2) I will show that most human
> variation occurs at the periphery of the network. (3) I will compare
> the topology and variation of the regulatory network to the call graph
> of a computer operating system, showing that they have different
> patterns of variation. (4) I will talk about web-based tools for the
> analysis of networks (TopNet and tYNA).
>
> http://networks.gersteinlab.org
> http://tyna.gersteinlab.org
>
> Comparing genomes to computer operating systems in terms of the
> topology and evolution of their regulatory control networks.
> KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
> Acad Sci U S A 107:9186-91.
>
> Analysis of diverse regulatory networks in a hierarchical context
> shows consistent tendencies for collaboration in the middle levels.
> N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
>
> Positive selection at the protein network periphery: evaluation in
> terms of structural constraints and cellular context.
> PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
>
> The tYNA platform for comparative interactomics: a web tool for
> managing, comparing and mining multiple networks.
> KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
--
Cathy H. Wu, Ph.D.
Edward G. Jefferson Chair of Bioinformatics& Computational Biology
Department of Computer& Information Sciences
Department of Biological Sciences
Director, Center for Bioinformatics& Computational Biology (CBCB)
Director, Master's Programs in Bioinformatics& Computational Biology
Director, Protein Information Resource (PIR)
Delaware Biotechnology Institute
University of Delaware
15 Innovation Way, Suite 205
Newark, DE 19711-5449
Email: wuc@udel.edu
Phone: 302-831-8869; Fax: 302-831-4841
Adm Assistant: Susan Phipps
Email: phipps@dbi.udel.edu
Phone: 302-831-0161
CBCB home: http://bioinformatics.udel.edu
Master's programs: http://bioinformatics.udel.edu/Education
PIR Home: http://ProteinInformationResource.org
Friday, May 18, 2012
Abstract for talk at CBCB Symposium at U Del ((* i0udcbcbrs *))
TITLE:
Molecular Networks: The Next-generation Annotation for Personal Genomes
Mark Gerstein
Yale University
My talk will be concerned the analysis of networks and the use of
networks as a "next-generation annotation" for interpreting personal
genomes. I will initially describe current approaches to genome
annotation in terms of one-dimension browser tracks. Then I will
describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of
the regulatory network indicates that it has a hierarchical layout
with the "middle-managers" acting as information-flow bottlenecks and
with more "influential" TFs on top. (2) I will show that most human
variation occurs at the periphery of the network. (3) I will compare
the topology and variation of the regulatory network to the call graph
of a computer operating system, showing that they have different
patterns of variation. (4) I will talk about web-based tools for the
analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the
topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context
shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in
terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for
managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
Molecular Networks: The Next-generation Annotation for Personal Genomes
Mark Gerstein
Yale University
My talk will be concerned the analysis of networks and the use of
networks as a "next-generation annotation" for interpreting personal
genomes. I will initially describe current approaches to genome
annotation in terms of one-dimension browser tracks. Then I will
describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of
the regulatory network indicates that it has a hierarchical layout
with the "middle-managers" acting as information-flow bottlenecks and
with more "influential" TFs on top. (2) I will show that most human
variation occurs at the periphery of the network. (3) I will compare
the topology and variation of the regulatory network to the call graph
of a computer operating system, showing that they have different
patterns of variation. (4) I will talk about web-based tools for the
analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the
topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context
shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in
terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for
managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
Thursday, May 10, 2012
Abstract for talk at CCBR at U Toronto ((* i0tor12 *))
TITLE:
Molecular Networks: The Next-generation Annotation for Personal Genomes
Mark Gerstein
Yale University
My talk will be concerned the analysis of networks and the use of
networks as a "next-generation annotation" for interpreting personal
genomes. I will initially describe current approaches to genome
annotation in terms of one-dimension browser tracks. Then I will
describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of
the regulatory network indicates that it has a hierarchical layout
with the "middle-managers" acting as information-flow bottlenecks and
with more "influential" TFs on top. (2) I will show that most human
variation occurs at the periphery of the network. (3) I will compare
the topology and variation of the regulatory network to the call graph
of a computer operating system, showing that they have different
patterns of variation. (4) I will talk about web-based tools for the
analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the
topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context
shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in
terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for
managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
Molecular Networks: The Next-generation Annotation for Personal Genomes
Mark Gerstein
Yale University
My talk will be concerned the analysis of networks and the use of
networks as a "next-generation annotation" for interpreting personal
genomes. I will initially describe current approaches to genome
annotation in terms of one-dimension browser tracks. Then I will
describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of
the regulatory network indicates that it has a hierarchical layout
with the "middle-managers" acting as information-flow bottlenecks and
with more "influential" TFs on top. (2) I will show that most human
variation occurs at the periphery of the network. (3) I will compare
the topology and variation of the regulatory network to the call graph
of a computer operating system, showing that they have different
patterns of variation. (4) I will talk about web-based tools for the
analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the
topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context
shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in
terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for
managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
Wednesday, May 2, 2012
Abstract for talk at Next Generation Sequencing for Drug Developers ((* i0ngenddev *))
TITLE:
Molecular Networks: The Next-generation Annotation for Personal Genomes
Mark Gerstein
Yale University
My talk will be concerned the analysis of networks and the use of
networks as a "next-generation annotation" for interpreting personal
genomes. I will initially describe current approaches to genome
annotation in terms of one-dimension browser tracks. Then I will
describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of
the regulatory network indicates that it has a hierarchical layout
with the "middle-managers" acting as information-flow bottlenecks and
with more "influential" TFs on top. (2) I will show that most human
variation occurs at the periphery of the network. (3) I will compare
the topology and variation of the regulatory network to the call graph
of a computer operating system, showing that they have different
patterns of variation. (4) I will talk about web-based tools for the
analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the
topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context
shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in
terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for
managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
Molecular Networks: The Next-generation Annotation for Personal Genomes
Mark Gerstein
Yale University
My talk will be concerned the analysis of networks and the use of
networks as a "next-generation annotation" for interpreting personal
genomes. I will initially describe current approaches to genome
annotation in terms of one-dimension browser tracks. Then I will
describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of
the regulatory network indicates that it has a hierarchical layout
with the "middle-managers" acting as information-flow bottlenecks and
with more "influential" TFs on top. (2) I will show that most human
variation occurs at the periphery of the network. (3) I will compare
the topology and variation of the regulatory network to the call graph
of a computer operating system, showing that they have different
patterns of variation. (4) I will talk about web-based tools for the
analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the
topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context
shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in
terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for
managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
Sunday, April 29, 2012
abstract for talk at Harvard Systems Biology [i0hsb]
TITLE:
Molecular Networks: The Next-generation Annotation for Personal Genomes
Mark Gerstein
Yale University
My talk will be concerned the analysis of networks and the use of
networks as a "next-generation annotation" for interpreting personal
genomes. I will initially describe current approaches to genome
annotation in terms of one-dimension browser tracks. Then I will
describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of
the regulatory network indicates that it has a hierarchical layout
with the "middle-managers" acting as information-flow bottlenecks and
with more "influential" TFs on top. (2) I will show that most human
variation occurs at the periphery of the network. (3) I will compare
the topology and variation of the regulatory network to the call graph
of a computer operating system, showing that they have different
patterns of variation. (4) I will talk about web-based tools for the
analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the
topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context
shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in
terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for
managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
Molecular Networks: The Next-generation Annotation for Personal Genomes
Mark Gerstein
Yale University
My talk will be concerned the analysis of networks and the use of
networks as a "next-generation annotation" for interpreting personal
genomes. I will initially describe current approaches to genome
annotation in terms of one-dimension browser tracks. Then I will
describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of
the regulatory network indicates that it has a hierarchical layout
with the "middle-managers" acting as information-flow bottlenecks and
with more "influential" TFs on top. (2) I will show that most human
variation occurs at the periphery of the network. (3) I will compare
the topology and variation of the regulatory network to the call graph
of a computer operating system, showing that they have different
patterns of variation. (4) I will talk about web-based tools for the
analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the
topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context
shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in
terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for
managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
Saturday, April 21, 2012
abstract for talk at UCLA [i0ucla]
TITLE:
Analysis of Molecular Networks
Mark Gerstein
Yale University
My talk will be concerned the analysis of networks and the use of
networks as a "next-generation annotation" for interpreting personal
genomes. I will initially describe current approaches to genome
annotation in terms of one-dimension browser tracks. Then I will
describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of
the regulatory network indicates that it has a hierarchical layout
with the "middle-managers" acting as information-flow bottlenecks and
with more "influential" TFs on top. (2) I will show that most human
variation occurs at the periphery of the network. (3) I will compare
the topology and variation of the regulatory network to the call graph
of a computer operating system, showing that they have different
patterns of variation. (4) I will talk about web-based tools for the
analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the
topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl
Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context
shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in
terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for
managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
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